whole genome sequencing data analysis
hello,
I checked the raw data by FASTQC and found red color: Per base sequence content,
Orange :per tiles sequence quality,
orange : per sequence duplication level,
do I need to do filtering or trimming? do I need to remove reads duplication?
kind response guys
• 857 views
•
link
updated
by
Biostar
•
written
by
ipb727258 •
•
written
by
ipb727258 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
why my fastqc on trimmed data failed?
written by kamran.kouchakzadeh.kk •
-
Fastp Trimming for WGS
written by j.k3096 •
-
alignment result
written by ahmad.sajad4541 •
-
FastQC per base to total base calculator
written by jimmy0958073736 •
-
Removing warning FASTQC
written by ipb727258 •
-
how to remove warning and failures observed inQuality report by Fastqc for RNA-Seq data
written by aiswaryabioinfo •
-
FastQC report analysis
written by anjuraas •
-
Quality report by Fastqc, Result Interpretation and Next step parameters
written by ravi.uhdnis
-
FastQ quality check : what can we correct ?
written by Rad
-
Ngs-Qc-Per Base Sequence Content Failed
written by williamjohn360
Please add images using these directions: How to add images to a Biostars post
As you give no details my comment is general, and I assume this is a WGS sample. If no adapter content is flagged by fastqc you generally do not need to trim anything. Duplicates are commonly removed after alignment, e.g. using samtools fixmate/markdup, Picard MarkDuplicates, samblaster or sambamba. Alternatively they can be removed prior to alignment e.g.
bbduk.shfrom BBMap suite. For a more elaborate answer you need to add some details.